Citrus Sinensis ID: 014482

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420---
Protein Sequence
MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQDFCSGDDE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHHHHHcccEEEEEEccEEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccEEEEccccccccHHHHHHHHHHHccEEEEEcccccccHHHHHHHHHHHHcccEEEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHccccccccccccEcccccccccccHHHcccccHHHcccccccccccccccccccccccccHccccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccHHHHHHHHHHHHccccccEEEcccccHHHHHHHHHHHHHHHccEEEEEEcccccHHHHHHHHHHHHHcccEEEEEcccEEEEEEcccccccccccccEEEccccccccHHHHccccccccHHHHHHHHHccccccHHHHHHHcccEEcHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccHHccccccc
Coil and Loop (DISEMBL)
mifnrfsrqkpslrsqpftlLTCCLsataanttnnssklydhysfkpppslspkpenpnptlnpnknfkkkskpqyrppssldapkkkytdlpfdfrysytetnqnvrpiglrepkyspfgpgrlerewtgvcapaadpkvksaeegaedpnleeKRILVREriqgepltnAERKALVEKCHRNRTKRQinlgrdglthNMLNDIHNHWKHAEAVRIKclgvptvdmknvcfqledktfgkiifrhGGTLVLyrgrnynpkkrpviplmlwrphepvypkLIKTTIEGLSIEETKEMRKRGLAVPVLTKlakngyygslvpMVRDAFLVSELVRIdcqglersdykkigcklrdlvPCILVTFEKEQIVVWrgkdykhpgddgqffthrelfddpendsacgveeevmgdsssqqdfcsgdde
Flexible Loop (DISEMBL)
mifnrfsrqkpslrsqpfTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTlnpnknfkkkskpqyrppssldapkkkytdLPFDFRYSYTetnqnvrpiglrepkYSPFGPGRLEREWTGVCAPaadpkvksaeegaedpnleekrilvreriqgepltnaerkalvekchrnrtkrqinlgrdglTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDktfgkiifrhggtlvlyrgrnynpkkrpviplmlwrphepvypkLIKTTIEGlsieetkemrkrglavpvLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCqglersdykkigcklRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEevmgdsssqqdfcsgdde
Low Complexity Region (SEG)
MIFNRFSRQKPSLRSQPFtlltcclsataanttnnssKLYDHYSFkpppslspkpenpnpTLnpnknfkkkskpQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQDFCSGDDE
Disordered region (IsUnstruct)
*****************FTLLTCCLSATAA***********************************************************TDLPFDFRYSYTETNQNVRPIGL************LEREWTGVC********************************************VEKCHR*RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHR**********************************
Disordered Region (DISOPRED)
*********************************************************************************************F************************P**********************************************************************INLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRP**********************EMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDY***********************************************
Disordered Region (DISEMBL)
*************RSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNF***************APKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPEND*************************
Disordered Region (DISPRO)
MIFNRFSR******S*PFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLS************************RPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVC******************************IQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYK**********************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQDFCSGDDE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	423	2.2.26 [Sep-21-2011]
Q8VYD9	405	CRS2-associated factor 1,	yes	no	0.926	0.967	0.705	1e-154
Q6Z4U2	428	CRS2-associated factor 1,	yes	no	0.794	0.785	0.676	1e-125
Q9FFU1	358	CRS2-associated factor 2,	no	no	0.645	0.762	0.559	5e-92
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.657	0.759	0.553	5e-86
Q9SL79	701	CRS2-associated factor 1,	no	no	0.721	0.435	0.476	2e-82
Q657G7	607	CRS2-associated factor 2,	no	no	0.664	0.462	0.503	4e-77
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.659	0.398	0.482	8e-77
Q9LDA9	564	CRS2-associated factor 2,	no	no	0.664	0.498	0.493	1e-76
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.664	0.459	0.490	1e-76
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.666	0.418	0.490	3e-76

>sp|Q8VYD9|CAF1M_ARATH CRS2-associated factor 1, mitochondrial OS=Arabidopsis thaliana GN=At4g31010 PE=2 SV=1

 Score =  544 bits (1401), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 285/404 (70%), Positives = 324/404 (80%), Gaps = 12/404 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP LS      NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPLSSSASE-NP 51

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPF
Sbjct: 52  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPF 111

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 112 GPDRLDREWTGVCAPAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 170

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 171 CQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 230

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 231 QVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 290

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCIL 360
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLRDLVPCIL
Sbjct: 291 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCIL 350

Query: 361 VTFEKEQIVVWRGKDYKHPGDDGQF--FTHRELFDDPENDSACG 402
           VTF+KEQ+V+WRGKDYK P +D ++  F HRE   D + D +C 
Sbjct: 351 VTFDKEQVVIWRGKDYKPPKEDDEYSSFIHRESSIDSDVDLSCS 394

May be involved for the splicing of group IIB introns in mitochondrions.
Arabidopsis thaliana (taxid: 3702)

>sp|Q6Z4U2|CAF1M_ORYSJ CRS2-associated factor 1, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0174900 PE=2 SV=1

 Score =  450 bits (1157), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 234/346 (67%), Positives = 272/346 (78%), Gaps = 10/346 (2%)

Query: 37  SKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKK--KYTDLPF 94
           S L D Y F PP SL+P     + + +     ++  KP YRPPSSLD   +    +DLPF
Sbjct: 23  SGLLDRYGFVPPASLTPH----SASDDGGAKKRRPKKPPYRPPSSLDRGGRPAARSDLPF 78

Query: 95  DFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLE 154
           DFR+SYTE++   +PIGLREPKYSPFGPGRL+R WTG+CAPA D  ++ A      P  E
Sbjct: 79  DFRFSYTESSPGDKPIGLREPKYSPFGPGRLDRPWTGLCAPAVDTTLRDAHADDPAPAAE 138

Query: 155 EKRILVRER----IQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWK 210
            +    R R    + GEPLT AER  LV KC ++RTK+QINLGRDGLTHNMLNDIHNHWK
Sbjct: 139 RELEEARRRERERVLGEPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWK 198

Query: 211 HAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLML 270
           + EAVR+KCLGVPTVDM+NVC QLEDKT G II RHGG L+LYRGR+YNPKKRPVIPLML
Sbjct: 199 NDEAVRVKCLGVPTVDMQNVCHQLEDKTGGLIIHRHGGQLILYRGRHYNPKKRPVIPLML 258

Query: 271 WRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVS 330
           W+P EPVYP+LIKTTIEGL++EETKEMRK+GL VPVLTKLAKNGYY SLVPMVRDAFL  
Sbjct: 259 WKPAEPVYPRLIKTTIEGLTVEETKEMRKKGLYVPVLTKLAKNGYYASLVPMVRDAFLTD 318

Query: 331 ELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDY 376
           ELVRID +GL +SDY+KIG KLRDLVPCI+V+F+KEQI+VWRGKDY
Sbjct: 319 ELVRIDSKGLPKSDYRKIGVKLRDLVPCIIVSFDKEQIIVWRGKDY 364

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FFU1|CAF2M_ARATH CRS2-associated factor 2, mitochondrial OS=Arabidopsis thaliana GN=At5g54890 PE=2 SV=1

 Score =  338 bits (867), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 160/286 (55%), Positives = 208/286 (72%), Gaps = 13/286 (4%)

Query: 90  TDLPFDFRYSYTETNQNVRPIGLREPK-YSPFGPGRLEREWTGVCAPAADPKVKSAEEGA 148
           +DLPFDFRYSY+ETN  + PIG REPK +SPFGPGRL+R+WTG  A  A P++  ++   
Sbjct: 75  SDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTA-LASPEIDQSQWVE 133

Query: 149 EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNH 208
           E           R R+ GE LT  E   L+E+   +   RQINLG+ G+THNM++DIHNH
Sbjct: 134 E-----------RARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNH 182

Query: 209 WKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPL 268
           WK AEAVRIKCLGVPT+DM N+CF LE+K+ GKI++R+   LVLYRGRNY+PK RP+IPL
Sbjct: 183 WKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPL 242

Query: 269 MLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFL 328
           MLW+PH P+YP+L+K   +GL  EETKEMR RGL  P L KL +NG Y ++V  VR+ F 
Sbjct: 243 MLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFE 302

Query: 329 VSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
             E+VR+DC  +  SD K+IG KL+++VPC+ + F+ EQI++WRGK
Sbjct: 303 TEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILWRGK 348

May be involved for the splicing of group IIB introns in mitochondrions.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0J7J7|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2

 Score =  318 bits (815), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 161/291 (55%), Positives = 206/291 (70%), Gaps = 13/291 (4%)

Query: 85  PKKKYTDLPFDFRYSYTETNQNVRPIGLREP-KYSPFGPGRLEREWTGVCAPAADPKVKS 143
           P+   +DLPFDFRYSY+ET+   RPIG REP ++SPFGPGRL+R W GV A AA  +   
Sbjct: 72  PEPASSDLPFDFRYSYSETDPAWRPIGFREPTRFSPFGPGRLDRPWDGVAAAAARGEGAG 131

Query: 144 AEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLN 203
           A   +            RE + GEPL   E   LVE+   +   RQINLG+ G+THNM++
Sbjct: 132 AAATS------------REEVLGEPLAEEEVAQLVERYRHSDCSRQINLGKGGVTHNMID 179

Query: 204 DIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKR 263
           DIHNHWK AEAVRIKCLGVPT+DM N+CF LEDKT GK+I+R+   L+LYRGRNY+PK+R
Sbjct: 180 DIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVIYRNINILILYRGRNYDPKQR 239

Query: 264 PVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMV 323
           P IPLMLW+P  P+YP+L++   +GL+ E+TKE+R  GL    L KL +NG Y ++V  V
Sbjct: 240 PQIPLMLWKPLAPIYPRLVQNVADGLTFEKTKELRNTGLNSSPLMKLTRNGVYVNVVDRV 299

Query: 324 RDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
           R+AF   E+VR+DC  +  SD KKIG KLRDLVPC+ + F+ EQI++WRGK
Sbjct: 300 REAFKTVEVVRLDCSHVGSSDCKKIGVKLRDLVPCVPLLFKDEQIILWRGK 350

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SL79|CAF1P_ARATH CRS2-associated factor 1, chloroplastic OS=Arabidopsis thaliana GN=At2g20020 PE=1 SV=2

 Score =  306 bits (783), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 160/336 (47%), Positives = 215/336 (63%), Gaps = 31/336 (9%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
           PF+F+YSYTET + V+P+ LREP Y+PFGP  + R WTG                    P
Sbjct: 150 PFEFKYSYTETPK-VKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLPP 208

Query: 136 AADPKVKSAEE-GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
                +K  ++ G   P +  + +  +E I GEPLT  E + LV  C +  T RQ+N+GR
Sbjct: 209 VGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLK--TTRQLNMGR 266

Query: 195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
           DGLTHNMLN+IH+ WK     +IKC GV TVDM NVC QLE+K  GK+I+R GG L L+R
Sbjct: 267 DGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFR 326

Query: 255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
           GRNYN + RP  PLMLW+P  PVYP+LI+   EGL+ +E   MR++G  +  + KL KNG
Sbjct: 327 GRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNG 386

Query: 315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
            Y  LV  V++AF V ELVRIDCQG++ SD++KIG KL+DLVPC+LV+FE EQI++WRG+
Sbjct: 387 VYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIWRGR 446

Query: 375 DYKH----PGDDGQFFTHRELFDDPENDSACGVEEE 406
           ++K     P   G      ++ +D E D+A   ++E
Sbjct: 447 EWKSSLTTPDKKG------DILEDIEVDTALPEDDE 476

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Arabidopsis thaliana (taxid: 3702)

>sp|Q657G7|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1

 Score =  288 bits (738), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 158/314 (50%), Positives = 203/314 (64%), Gaps = 33/314 (10%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGA---- 148
           PFDFR+SY+E  +   P+ +REP + PF P  + R WTG  AP    + K+   G     
Sbjct: 127 PFDFRFSYSECPR-APPVAIREPAFLPFAPPTMPRPWTGK-APLLTKEEKARRRGVRLHT 184

Query: 149 ----EDP----------------NLEEKRIL-----VRERIQGEPLTNAERKALVEKCHR 183
               E P                 L+  R+       RE + GEPLT AE + LV K H 
Sbjct: 185 PLGEEAPRTVSAHGIMMEVRGRRKLDLARVSPGDGRSREEVLGEPLTAAEVRDLV-KPHI 243

Query: 184 NRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKII 243
           +   RQ+N+GRDGLTHNML  IH HW+  E  +++C GVPTVDMKN+C+ LE+K+ GK+I
Sbjct: 244 SHN-RQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKVI 302

Query: 244 FRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLA 303
            R GG + LYRGRNYNP+ RP  PLMLW+P  PVYPKLI+   EGL+ EE  EMR+RG  
Sbjct: 303 HRVGGVVFLYRGRNYNPRTRPRYPLMLWKPATPVYPKLIQEAPEGLTKEEADEMRRRGKD 362

Query: 304 VPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTF 363
           +  + KLAKNG Y  LV  VRDAF  S+LV+IDC+GL  SDYKKIG KLRDLVPC+L++F
Sbjct: 363 LLPICKLAKNGIYIYLVRDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLSF 422

Query: 364 EKEQIVVWRGKDYK 377
           + EQI+++RGK++K
Sbjct: 423 DNEQILMFRGKEWK 436

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q5VMQ5|CAF1P_ORYSJ CRS2-associated factor 1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0495900 PE=2 SV=1

 Score =  288 bits (736), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 148/307 (48%), Positives = 193/307 (62%), Gaps = 28/307 (9%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG-----------------VCAP 135
           PF+F+YSYTET +  RP+ LRE  + PFGP    R WTG                 +  P
Sbjct: 91  PFEFQYSYTETPR-ARPVALREAPFLPFGPEVTPRPWTGRKPLPKSRKELPEFDSFMLPP 149

Query: 136 AADPKVKSAEE-----GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQI 190
                VK  +         +P  +      RE + GEPLT  E   LV+     +TKRQ+
Sbjct: 150 PGKKGVKPVQSPGPFLAGTEPRYQAAS---REEVLGEPLTKEEVDELVKATL--KTKRQL 204

Query: 191 NLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTL 250
           N+GRDGLTHNML +IH+HWK     +IKC GV TVDM NVC QLE+K  GK+I   GG +
Sbjct: 205 NIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMDNVCQQLEEKVGGKVIHHQGGVI 264

Query: 251 VLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKL 310
            L+RGRNYN + RP+ PLMLW+P  PVYP+L+K   +GL+ +E ++MRKRG  +P + KL
Sbjct: 265 FLFRGRNYNYRTRPIYPLMLWKPAAPVYPRLVKKIPDGLTPDEAEDMRKRGRQLPPICKL 324

Query: 311 AKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVV 370
            KNG Y +LV  VR+AF   +LVR+DC GL +SD +KIG KL+DLVPC L++FE E I++
Sbjct: 325 GKNGVYLNLVKQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCTLLSFEFEHILM 384

Query: 371 WRGKDYK 377
           WRG D+K
Sbjct: 385 WRGNDWK 391

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LDA9|CAF2P_ARATH CRS2-associated factor 2, chloroplastic OS=Arabidopsis thaliana GN=At1g23400 PE=2 SV=1

 Score =  287 bits (735), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 150/304 (49%), Positives = 197/304 (64%), Gaps = 23/304 (7%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
           PF+F++SY+ET + V+P+G+REP + PF P  + R WTG                    P
Sbjct: 110 PFEFQFSYSETPK-VKPVGIREPAFMPFAPPTMPRPWTGKAPLKKSKKKIPLFDSFNPPP 168

Query: 136 AADPKVKSAEEGAEDP-NLEEKRILVRERIQGEPLTNAERKALVE-KCHRNRTKRQINLG 193
           A    VK  E     P     K  + RE + GEPL   E+  L++   H NR   Q+NLG
Sbjct: 169 AGKSGVKYVEMPGPLPFGRYPKEGMNREEVLGEPLKRWEKGMLIKPHMHDNR---QVNLG 225

Query: 194 RDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLY 253
           RDG THNML  IH+HWK     +++C GVPTVDM NVC  LE+KT G+II R GG + L+
Sbjct: 226 RDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLF 285

Query: 254 RGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKN 313
           RGRNYN + RP  PLMLW+P  PVYPKLI+   EGL+ EE  E R +G ++  + KL+KN
Sbjct: 286 RGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKN 345

Query: 314 GYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRG 373
           G Y SLV  VRDAF +S LV++DC GLE SDYKKIG KL++LVPC+L++F+ EQI++WRG
Sbjct: 346 GVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQILMWRG 405

Query: 374 KDYK 377
           +++K
Sbjct: 406 REWK 409

Essential protein required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84N48|CAF2P_MAIZE CRS2-associated factor 2, chloroplastic OS=Zea mays GN=CAF2 PE=1 SV=1

 Score =  287 bits (734), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 154/314 (49%), Positives = 204/314 (64%), Gaps = 33/314 (10%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGA---- 148
           PFDF++SY+E  +   P+ +REP + PF P  + R WTG  AP    + K+   G     
Sbjct: 131 PFDFQFSYSEAPR-APPLAIREPAFLPFAPPTMPRPWTG-KAPLLTKEEKARRRGVRLHT 188

Query: 149 ----EDPN----------LEEKRIL-----------VRERIQGEPLTNAERKALVEKCHR 183
               E P           + E+R +            RE + GEPLT +E +ALV K H 
Sbjct: 189 PLGQETPQTVSAHGIMMEVRERRKMDLARVSPGDGRSREEVLGEPLTPSEVRALV-KPHI 247

Query: 184 NRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKII 243
           +   RQ+N+GRDGLTHNML  IH HW+  E  +++C GVPTVDMKN+C+ LE+K+ GK+I
Sbjct: 248 SHN-RQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKVI 306

Query: 244 FRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLA 303
            R GG + LYRGR+Y+PK RP  PLMLW+P  PVYPKLIK   +G + EE  EMR++G  
Sbjct: 307 HRVGGVVFLYRGRHYDPKTRPRYPLMLWKPATPVYPKLIKEAPDGFTKEEADEMRRKGRD 366

Query: 304 VPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTF 363
           +  + KLAKNG Y +LV  VRDAF  S+LV+IDC+GL  SDYKKIG KLRDLVPC+L++F
Sbjct: 367 LLPICKLAKNGIYITLVKDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLSF 426

Query: 364 EKEQIVVWRGKDYK 377
           + EQI++ RGK++K
Sbjct: 427 DDEQILMHRGKEWK 440

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

>sp|Q84N49|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 SV=1

 Score =  285 bits (730), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 149/304 (49%), Positives = 193/304 (63%), Gaps = 22/304 (7%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG----------------VCAPA 136
           PF+F+YSYTE  +  RP+ LRE  + PFGP    R WTG                   PA
Sbjct: 91  PFEFQYSYTEAPR-ARPVALREAPFMPFGPEATPRPWTGRKPLPKSRKELPEFDSFVLPA 149

Query: 137 ADPK-VKSAEE-GAEDPNLEEK-RILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLG 193
              K VK  +  G     +E + + + RE I GEPLT  E   LV+   +  +KRQ+N+G
Sbjct: 150 PGKKGVKPVQSPGPFLAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLK--SKRQLNMG 207

Query: 194 RDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLY 253
           RDGLTHNML +IH+HWK     +IKC GV T+DM N+C QLE+K  GK+I R GG + L+
Sbjct: 208 RDGLTHNMLENIHSHWKRKRVCKIKCKGVCTIDMDNICHQLEEKVGGKVIHRQGGVIFLF 267

Query: 254 RGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKN 313
           RGRNYN + RP  PLMLW+P  PVYP+L+     GL+ +E  EMR RG  +P + KL KN
Sbjct: 268 RGRNYNYRTRPCFPLMLWKPVAPVYPRLVTKVPGGLTPDEATEMRTRGHQLPPICKLGKN 327

Query: 314 GYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRG 373
           G Y +LV  VR+AF   +LVR+DC GL +SD +KIG KL+DLVPCIL++FE E I++WRG
Sbjct: 328 GVYANLVNQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCILLSFEFEHILMWRG 387

Query: 374 KDYK 377
            D+K
Sbjct: 388 SDWK 391

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	423
317106625	415	JHL05D22.2 [Jatropha curcas]	0.969	0.987	0.745	1e-177
255541412	411	conserved hypothetical protein [Ricinus	0.959	0.987	0.730	1e-168
225453847	418	PREDICTED: CRS2-associated factor 1, mit	0.978	0.990	0.727	1e-164
224130086	405	predicted protein [Populus trichocarpa]	0.929	0.970	0.719	1e-159
356560247	396	PREDICTED: CRS2-associated factor 1, mit	0.886	0.946	0.704	1e-155
297802930	408	DNA binding protein [Arabidopsis lyrata	0.929	0.963	0.702	1e-154
22329043	405	CRS2-associated factor 1 [Arabidopsis th	0.926	0.967	0.705	1e-152
449432211	392	PREDICTED: CRS2-associated factor 1, mit	0.770	0.831	0.803	1e-150
357144801	437	PREDICTED: CRS2-associated factor 1, mit	0.791	0.766	0.693	1e-136
326525102	443	predicted protein [Hordeum vulgare subsp	0.900	0.860	0.621	1e-134

>gi|317106625|dbj|BAJ53131.1| JHL05D22.2 [Jatropha curcas]

 Score =  627 bits (1616), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 317/425 (74%), Positives = 354/425 (83%), Gaps = 15/425 (3%)

Query: 2   IFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPK-PENPNP 60
           +  R SRQKP     P + L   L A   ++ + SSKL+DHY+F+PPPSLSP+ P+NPNP
Sbjct: 3   LLARLSRQKPP----PPSSLCLTLLARHLSSASTSSKLHDHYAFRPPPSLSPQEPDNPNP 58

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYS 118
           T       +KK KP YRPPS+LD   KK  ++DLPFDFRYSYTE++Q+VRPIGLREPKYS
Sbjct: 59  TT------RKKQKPLYRPPSTLDRTGKKPTHSDLPFDFRYSYTESSQSVRPIGLREPKYS 112

Query: 119 PFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALV 178
           PFGP RL+R WTGVCAPA DPKVKS + G +DPNLEEKR L+RE+IQG+PLTNAERK LV
Sbjct: 113 PFGPDRLDRSWTGVCAPAVDPKVKSLD-GTDDPNLEEKRKLMREKIQGDPLTNAERKILV 171

Query: 179 EKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKT 238
            +C RN+TKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVC QLEDKT
Sbjct: 172 AQCQRNKTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCSQLEDKT 231

Query: 239 FGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMR 298
           FGKII RH G+LVLYRGRNYNPKKRPVIPLM+WRPHEP+YP+LIKTTI+GLSI+ETKEMR
Sbjct: 232 FGKIIHRHCGSLVLYRGRNYNPKKRPVIPLMMWRPHEPIYPRLIKTTIDGLSIDETKEMR 291

Query: 299 KRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPC 358
           KRGLAVP LTKLAKNGYY SLVPMVRDAFL +ELVRIDCQGLE+SDYKKIGCKLRDLVPC
Sbjct: 292 KRGLAVPALTKLAKNGYYASLVPMVRDAFLTNELVRIDCQGLEKSDYKKIGCKLRDLVPC 351

Query: 359 ILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQDFC 418
           ILVTFEKEQIVVWRGKDYK P +DG+ F  RE FDDPE  S    E+    D +S   F 
Sbjct: 352 ILVTFEKEQIVVWRGKDYK-PPEDGELFADREFFDDPEGSSMGLSEDSCSSDDNSSPGFY 410

Query: 419 SGDDE 423
           SGDDE
Sbjct: 411 SGDDE 415

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541412|ref|XP_002511770.1| conserved hypothetical protein [Ricinus communis] gi|223548950|gb|EEF50439.1| conserved hypothetical protein [Ricinus communis]

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/426 (73%), Positives = 348/426 (81%), Gaps = 20/426 (4%)

Query: 1   MIFNRFSRQKPSLRSQPF-TLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPN 59
           ++ NR SR+KP     P+ TLL+  LS+ +A     SSKL+D YSF PPPSLSP+     
Sbjct: 2   LLLNRLSREKP-----PYPTLLSRYLSSASA-----SSKLHDQYSFMPPPSLSPQNHQ-- 49

Query: 60  PTLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKY 117
              NPN   KKK KP YRPPSSLD   KK  ++DLPFDFRYSYTE++Q+VRPIGLREPKY
Sbjct: 50  ---NPNSTPKKKRKPLYRPPSSLDRTGKKPTHSDLPFDFRYSYTESSQSVRPIGLREPKY 106

Query: 118 SPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKAL 177
           SPFGP RL+R WTGVCAP  +PK+K  + G+E+PNLEEKR   RE+IQG+PLTNAERK L
Sbjct: 107 SPFGPDRLDRAWTGVCAPVVEPKLKFVD-GSENPNLEEKRRWWREQIQGQPLTNAERKIL 165

Query: 178 VEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDK 237
           VE C R++TK+QINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVC QLEDK
Sbjct: 166 VESCQRHKTKKQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCTQLEDK 225

Query: 238 TFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEM 297
           TFGKII RH G LVLYRGRNY+PKKRPVIPLM+WRPHEP+YPKLIKTTIEGLSIEETKEM
Sbjct: 226 TFGKIIHRHCGLLVLYRGRNYHPKKRPVIPLMMWRPHEPIYPKLIKTTIEGLSIEETKEM 285

Query: 298 RKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVP 357
           RK+GLA+P LTKLAKNGYY SLVPMVRDAFLV+ELVRIDCQGL +SDYKKIGCKLRDLVP
Sbjct: 286 RKKGLALPALTKLAKNGYYASLVPMVRDAFLVNELVRIDCQGLPKSDYKKIGCKLRDLVP 345

Query: 358 CILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQDF 417
           CILVTFEKEQIVVWRGKDYK P + GQ F  RE FDDPE++     E     +S+  QDF
Sbjct: 346 CILVTFEKEQIVVWRGKDYK-PPEYGQSFVDRECFDDPESNEEYSKESCSSDESNDHQDF 404

Query: 418 CSGDDE 423
            S  DE
Sbjct: 405 YSSSDE 410

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453847|ref|XP_002272563.1| PREDICTED: CRS2-associated factor 1, mitochondrial [Vitis vinifera] gi|296089125|emb|CBI38828.3| unnamed protein product [Vitis vinifera]

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/426 (72%), Positives = 340/426 (79%), Gaps = 12/426 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
            I  RFSRQ     S   TL T  LS++A  +   SS+L DHYSFK P  +SP  +NPNP
Sbjct: 2   FIVTRFSRQIRQSHSAAVTLSTRRLSSSAPPSP--SSRLLDHYSFKSP--VSPF-QNPNP 56

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYS 118
             NP  + KKK KP YRPPSSLD   KK   +DLPFDFRYSYTE++  VRPIGLREPKYS
Sbjct: 57  --NPEPSTKKKQKPPYRPPSSLDRTGKKPLRSDLPFDFRYSYTESSPAVRPIGLREPKYS 114

Query: 119 PFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALV 178
           PFGPG L+REWTGVCAPA DPKV+S + G EDP LEEKR  +RE+  GEPLT AERK LV
Sbjct: 115 PFGPGLLDREWTGVCAPAVDPKVRSVD-GKEDPKLEEKRRRMREKTLGEPLTAAERKILV 173

Query: 179 EKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKT 238
           EKC R+RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKC+GVPTVDMKNVC QLEDKT
Sbjct: 174 EKCQRHRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCMGVPTVDMKNVCTQLEDKT 233

Query: 239 FGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMR 298
            GK+I R GG LVLYRGRNY+PKKRPVIPLMLWRPHEP+YP+LIKT I+GLSIEETKEMR
Sbjct: 234 SGKVIHRQGGLLVLYRGRNYHPKKRPVIPLMLWRPHEPIYPRLIKTVIDGLSIEETKEMR 293

Query: 299 KRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPC 358
           KRGLAVP LTKLAKNGYYGSLVPMVRDAFL  EL+RIDCQGLER DYKKIGCKLRD VPC
Sbjct: 294 KRGLAVPALTKLAKNGYYGSLVPMVRDAFLTDELIRIDCQGLERRDYKKIGCKLRDFVPC 353

Query: 359 ILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRELFDDPENDSACGVEEEVMGDSS-SQQDF 417
           ILVTFEKEQIVVWRGKDYK P + GQF   RE  D+ ++D   G ++    D S SQ  F
Sbjct: 354 ILVTFEKEQIVVWRGKDYK-PTEAGQFPIERESLDNWDSDMVYGGKQHKRSDDSCSQLAF 412

Query: 418 CSGDDE 423
            SGD+E
Sbjct: 413 YSGDEE 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130086|ref|XP_002320749.1| predicted protein [Populus trichocarpa] gi|222861522|gb|EEE99064.1| predicted protein [Populus trichocarpa]

 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 293/407 (71%), Positives = 335/407 (82%), Gaps = 14/407 (3%)

Query: 13  LRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKS 72
           L  Q    LT  LS++ A     SSKL+D Y FKPPPSLSP+     P  + N N KKK 
Sbjct: 7   LSGQKHFFLTRHLSSSTA-----SSKLHDIYCFKPPPSLSPE----KPQTSNNNNNKKKQ 57

Query: 73  KPQYRPPSSLDAPKKKY-TDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG 131
           KP+YRPPSSL+  KK   +DLPFDFR+SYTE+  +VRPIGLREPKYSPFGPGRL+R WTG
Sbjct: 58  KPEYRPPSSLETNKKPLRSDLPFDFRFSYTESCPDVRPIGLREPKYSPFGPGRLDRTWTG 117

Query: 132 VCAPAADPKVKSAEEGA--EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQ 189
           VCAPA D KVKS ++G   E  +LEEKR ++RE+IQG+PLT AE K LV+KC RN+TK+Q
Sbjct: 118 VCAPAVDLKVKSVDDGVGEEGLDLEEKRTVMREKIQGKPLTKAEGKILVDKCQRNKTKKQ 177

Query: 190 INLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGT 249
           INLG DGLTHNMLNDIHNHWKH EAVR+KC+GVPTVDMKNVC QLEDKTFGKII RH G 
Sbjct: 178 INLGIDGLTHNMLNDIHNHWKHDEAVRVKCMGVPTVDMKNVCTQLEDKTFGKIIHRHCGL 237

Query: 250 LVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTK 309
           LVLYRGRNY+P+ RPVIPLMLW+PHEPVYP+LIKTTI+GLSIEETKEMRKRGLAVP LTK
Sbjct: 238 LVLYRGRNYHPRNRPVIPLMLWKPHEPVYPRLIKTTIDGLSIEETKEMRKRGLAVPALTK 297

Query: 310 LAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIV 369
           L++NGY+GSLVPMVRDAFLVSELVRIDCQGL+RSD KKIGCKLRDLVPCILVTF+KEQIV
Sbjct: 298 LSRNGYFGSLVPMVRDAFLVSELVRIDCQGLDRSDSKKIGCKLRDLVPCILVTFDKEQIV 357

Query: 370 VWRGKDYKHPGD-DGQFFTHRELFDDPENDSACGVEEEVMGDSSSQQ 415
           VWRGKDYK P D DG FF  R+ FDDP++D  C ++E++  D +  Q
Sbjct: 358 VWRGKDYKPPEDEDGLFFADRQPFDDPQSDMDC-IKEKLSSDETRFQ 403

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560247|ref|XP_003548405.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Glycine max]

 Score =  553 bits (1424), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 277/393 (70%), Positives = 318/393 (80%), Gaps = 18/393 (4%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
            +  R +RQ PS      TLLT  LS+ A       SKL+ +Y+FKPP SL+P+P+  N 
Sbjct: 2   FLLTRLTRQNPSRA----TLLTRHLSSAA-------SKLHSNYTFKPPSSLAPQPQCSN- 49

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK---YTDLPFDFRYSYTETNQNVRPIGLREPKY 117
              P+K  +KK KP+YRPPSSLD   +K     DLPFDFR+SYTE++  VRPIGLREPKY
Sbjct: 50  -FPPSKPNQKKPKPRYRPPSSLDQAGRKPVRSNDLPFDFRFSYTESSAKVRPIGLREPKY 108

Query: 118 SPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKAL 177
           SPFGPGR++R+WTGVCAPA DP V+S E G EDP LEE+R   RE IQG+PL++ ERKAL
Sbjct: 109 SPFGPGRVDRKWTGVCAPAVDPTVESLE-GPEDPKLEEQRKKKREMIQGKPLSSEERKAL 167

Query: 178 VEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDK 237
           V +  R++T R +NLGRDGLTHNMLN IHNHWK AEAVRIKC+GVPT+DM N+C QLEDK
Sbjct: 168 VSQFERSKTNRHVNLGRDGLTHNMLNVIHNHWKFAEAVRIKCMGVPTMDMNNICTQLEDK 227

Query: 238 TFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEM 297
           TFGK+IFRHGGTL+LYRGRNYNPKKRPVIP+MLW+PHEPVYP+LIKTTI+GLSI+ETKEM
Sbjct: 228 TFGKVIFRHGGTLILYRGRNYNPKKRPVIPVMLWKPHEPVYPRLIKTTIDGLSIKETKEM 287

Query: 298 RKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVP 357
           RKRGL+VP LTKLAKNGYY  LVPMVRDAFL  ELVRIDC+GLER DYKKIGCKLRD+VP
Sbjct: 288 RKRGLSVPALTKLAKNGYYAFLVPMVRDAFLSCELVRIDCEGLERKDYKKIGCKLRDMVP 347

Query: 358 CILVTFEKEQIVVWRGKDYKHPGDDGQFFTHRE 390
           CILVTFE EQIVVWRGKDYKHP  DG F   RE
Sbjct: 348 CILVTFENEQIVVWRGKDYKHP-KDGYFLKDRE 379

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297802930|ref|XP_002869349.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297315185|gb|EFH45608.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata]

 Score =  550 bits (1416), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 284/404 (70%), Positives = 324/404 (80%), Gaps = 11/404 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP       + NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPPLSSSASENP 52

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE++ NVRPIGLREPKYSPF
Sbjct: 53  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESSSNVRPIGLREPKYSPF 112

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA DPKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 113 GPDRLDREWTGVCAPAVDPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 171

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLNDI+NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 172 CQRNKTKRQVNLGRDGLTHNMLNDIYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 231

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 232 QVVSKHCGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 291

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCIL 360
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GL+R DYKKIG KLRDLVPCIL
Sbjct: 292 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLDRKDYKKIGAKLRDLVPCIL 351

Query: 361 VTFEKEQIVVWRGKDYKHPGDDGQF--FTHRELFDDPENDSACG 402
           VTF+KEQ+V+WRGK+YK P DD ++  F HRE   D + D +C 
Sbjct: 352 VTFDKEQVVIWRGKNYKPPKDDDEYSSFIHRESSIDSDGDLSCS 395

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22329043|ref|NP_194830.2| CRS2-associated factor 1 [Arabidopsis thaliana] gi|75161464|sp|Q8VYD9.1|CAF1M_ARATH RecName: Full=CRS2-associated factor 1, mitochondrial; Flags: Precursor gi|18176015|gb|AAL59968.1| unknown protein [Arabidopsis thaliana] gi|20465409|gb|AAM20129.1| unknown protein [Arabidopsis thaliana] gi|332660446|gb|AEE85846.1| CRS2-associated factor 1 [Arabidopsis thaliana]

 Score =  544 bits (1401), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 285/404 (70%), Positives = 324/404 (80%), Gaps = 12/404 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP LS      NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPLSSSASE-NP 51

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPF
Sbjct: 52  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPF 111

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 112 GPDRLDREWTGVCAPAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 170

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 171 CQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 230

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 231 QVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 290

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCIL 360
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLRDLVPCIL
Sbjct: 291 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCIL 350

Query: 361 VTFEKEQIVVWRGKDYKHPGDDGQF--FTHRELFDDPENDSACG 402
           VTF+KEQ+V+WRGKDYK P +D ++  F HRE   D + D +C 
Sbjct: 351 VTFDKEQVVIWRGKDYKPPKEDDEYSSFIHRESSIDSDVDLSCS 394

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432211|ref|XP_004133893.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Cucumis sativus] gi|449480099|ref|XP_004155799.1| PREDICTED: LOW QUALITY PROTEIN: CRS2-associated factor 1, mitochondrial-like [Cucumis sativus]

 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 266/331 (80%), Positives = 291/331 (87%), Gaps = 5/331 (1%)

Query: 80  SSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAA 137
           SSLD   KK   ++LPFDF+YSYTET+ +VRPIGLREPKYSPFGPGRL+REWTGVCAPAA
Sbjct: 63  SSLDLGGKKPRRSNLPFDFQYSYTETSPSVRPIGLREPKYSPFGPGRLDREWTGVCAPAA 122

Query: 138 DPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGL 197
           +PK  S E G EDP LE KR ++RE IQGEPL  AERKALVEKC +N+TKRQINLGRDGL
Sbjct: 123 NPKATSVE-GMEDPRLEGKRRVMREAIQGEPLPGAERKALVEKCQKNKTKRQINLGRDGL 181

Query: 198 THNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRN 257
           THNMLNDIHNHW+H EAVRIKCLGVPTVDMKNVC QLEDKTFGKII RHGG LVLYRGRN
Sbjct: 182 THNMLNDIHNHWRHGEAVRIKCLGVPTVDMKNVCTQLEDKTFGKIIHRHGGFLVLYRGRN 241

Query: 258 YNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYG 317
           YNPKKRP IPLMLWRPHEP+YP+LIKTTI+GLSI+ETKEMRK+GLAVP LTKLAKNGYYG
Sbjct: 242 YNPKKRPFIPLMLWRPHEPIYPRLIKTTIDGLSIDETKEMRKKGLAVPALTKLAKNGYYG 301

Query: 318 SLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYK 377
           SLVPMVRDAFL  ELVRIDC+GLERSDYKKIGCKLRDLVPCILVTF+KEQIVVWRGKDY+
Sbjct: 302 SLVPMVRDAFLSCELVRIDCKGLERSDYKKIGCKLRDLVPCILVTFDKEQIVVWRGKDYQ 361

Query: 378 HPGDDGQFFTHRELFDDPENDSACGVEEEVM 408
            P D G + T RE FDD + ++ C  +E VM
Sbjct: 362 -PLDTG-YLTVRETFDDVDGNTGCVDDEVVM 390

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357144801|ref|XP_003573418.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Brachypodium distachyon]

 Score =  492 bits (1267), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 242/349 (69%), Positives = 282/349 (80%), Gaps = 14/349 (4%)

Query: 37  SKLYDHYSFKPPPSLSPKP-ENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKK--KYTDLP 93
           S+L DHY F PP SL+P P E P+      +  KK   P YRPPSSLD   +   ++DLP
Sbjct: 22  SRLLDHYGFAPPASLTPNPREAPHAAAEKKRRTKK---PPYRPPSSLDRGGRPASHSDLP 78

Query: 94  FDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDP-- 151
           FDFR+SYTE+  + +PIGLREPKYSPFGPGRL+R WTG+CAPA D  ++     AEDP  
Sbjct: 79  FDFRFSYTESTPDAKPIGLREPKYSPFGPGRLDRPWTGLCAPAVDTTIRDVH--AEDPAP 136

Query: 152 ----NLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHN 207
               +L+E R   RER+ GEPLT AER  +V+KC RNRTKRQ+NLGRDGLTHNMLNDIHN
Sbjct: 137 AAEKDLQEARRRERERVLGEPLTPAERTFVVDKCQRNRTKRQVNLGRDGLTHNMLNDIHN 196

Query: 208 HWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
           HWKH EAVR+KCLGVPTVDM+NVC +LEDKT G II RHGG L+LYRGR+Y+PKKRPVIP
Sbjct: 197 HWKHGEAVRVKCLGVPTVDMQNVCHELEDKTGGLIIHRHGGQLILYRGRHYHPKKRPVIP 256

Query: 268 LMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAF 327
           LMLW+P EP+YP+LIKTTIEGL++ ETK MRK+GL VPVLTKLAKNGYY SLVPMVRDAF
Sbjct: 257 LMLWKPAEPIYPRLIKTTIEGLTVVETKAMRKKGLHVPVLTKLAKNGYYASLVPMVRDAF 316

Query: 328 LVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDY 376
           L  ELVRIDC+GL +SDY+KIG KLRDLVPCILV+F+KEQI++WRGKDY
Sbjct: 317 LTDELVRIDCKGLPKSDYRKIGVKLRDLVPCILVSFDKEQIIIWRGKDY 365

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326525102|dbj|BAK07821.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  483 bits (1242), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 246/396 (62%), Positives = 297/396 (75%), Gaps = 15/396 (3%)

Query: 37  SKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSK-PQYRPPSSLDAPKK--KYTDLP 93
           S+L D Y F PP SL+P  +  +         K+++K P YRPPSSLD   +   ++DLP
Sbjct: 24  SRLLDLYGFVPPASLTPTAKEISHGTGAAAGQKRRTKKPPYRPPSSLDRGDRPASHSDLP 83

Query: 94  FDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDP-- 151
           FDFR+SYTE++ + +PIGLREPKYSPFGPGRL+R W+G+CAPA D  ++S +  AEDP  
Sbjct: 84  FDFRFSYTESSLDAKPIGLREPKYSPFGPGRLDRPWSGLCAPAVDTTLRSVD--AEDPAP 141

Query: 152 ----NLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHN 207
               +LEE R   RER+ GEPLT AER  LVEKC +NRTKRQINLGRDGLTHNMLNDIHN
Sbjct: 142 AAEKDLEEARRRERERVLGEPLTPAERSFLVEKCQKNRTKRQINLGRDGLTHNMLNDIHN 201

Query: 208 HWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
           HWKH E VR+KCLGVPTVDM+NVC +LEDKT G II RHGG L+LYRGR+Y+PKKRPVIP
Sbjct: 202 HWKHGEGVRVKCLGVPTVDMQNVCHELEDKTGGLIIHRHGGQLILYRGRHYHPKKRPVIP 261

Query: 268 LMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAF 327
           LMLW+P EP+YP+LIKTTIEGL++EETKEMRK+GL   VLTKLAKNGYY SLVPMVRD F
Sbjct: 262 LMLWKPAEPIYPRLIKTTIEGLTVEETKEMRKKGLHASVLTKLAKNGYYASLVPMVRDGF 321

Query: 328 LVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGKDYKHPGDDGQFFT 387
           L  ELVRIDC+GL +SDY+KIG KLRDLVPCILV+F+KEQI+VWRGKD+     D     
Sbjct: 322 LTDELVRIDCKGLPKSDYRKIGVKLRDLVPCILVSFDKEQIIVWRGKDHDESIQDNMHKA 381

Query: 388 HRELFDDPENDSACGVEEEVMGDSSSQQDFCSGDDE 423
              +        + GV+ E +    +  +  +G+DE
Sbjct: 382 SPSVL----QLESAGVKNENVEQEEASSESAAGEDE 413

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	423
TAIR|locus:2126694	405	AT4G31010 [Arabidopsis thalian	0.770	0.804	0.768	1.9e-140
TAIR|locus:2160195	358	AT5G54890 [Arabidopsis thalian	0.645	0.762	0.562	9.9e-87
TAIR|locus:2061604	701	CAF1 [Arabidopsis thaliana (ta	0.730	0.440	0.475	3.9e-76
TAIR|locus:2028100	564	CAF2 [Arabidopsis thaliana (ta	0.666	0.5	0.501	2e-72
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.174	0.073	0.378	2.5e-11
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.321	0.160	0.306	7.3e-10
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.208	0.099	0.355	4.4e-09
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.276	0.238	0.245	5e-05
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.274	0.161	0.291	0.00052

TAIR|locus:2126694 AT4G31010 [Arabidopsis thaliana (taxid:3702)]

 Score = 1374 (488.7 bits), Expect = 1.9e-140, P = 1.9e-140
 Identities = 253/329 (76%), Positives = 287/329 (87%)

Query:    75 QYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA 134
             QYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPFGP RL+REWTGVCA
Sbjct:    66 QYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPFGPDRLDREWTGVCA 125

Query:   135 PAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
             PA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE C RN+TKRQ+NLGR
Sbjct:   126 PAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVELCQRNKTKRQVNLGR 184

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG+++ +H GTLVLYR
Sbjct:   185 DGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFGQVVSKHSGTLVLYR 244

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+GLAVP LTKLAKNG
Sbjct:   245 GRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKKGLAVPALTKLAKNG 304

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
             YYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLRDLVPCILVTF+KEQ+V+WRGK
Sbjct:   305 YYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFDKEQVVIWRGK 364

Query:   375 DYKHPGDDGQF--FTHRELFDDPENDSAC 401
             DYK P +D ++  F HRE   D + D +C
Sbjct:   365 DYKPPKEDDEYSSFIHRESSIDSDVDLSC 393

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0010048 "vernalization response" evidence=RCA

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2160195 AT5G54890 [Arabidopsis thaliana (taxid:3702)]

 Score = 867 (310.3 bits), Expect = 9.9e-87, P = 9.9e-87
 Identities = 161/286 (56%), Positives = 210/286 (73%)

Query:    90 TDLPFDFRYSYTETNQNVRPIGLREPK-YSPFGPGRLEREWTGVCAPAADPKVKSAEEGA 148
             +DLPFDFRYSY+ETN  + PIG REPK +SPFGPGRL+R+WTG  A  A P++  ++   
Sbjct:    75 SDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTA-LASPEIDQSQW-- 131

Query:   149 EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNH 208
                 +EE     R R+ GE LT  E   L+E+   +   RQINLG+ G+THNM++DIHNH
Sbjct:   132 ----VEE-----RARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNH 182

Query:   209 WKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPL 268
             WK AEAVRIKCLGVPT+DM N+CF LE+K+ GKI++R+   LVLYRGRNY+PK RP+IPL
Sbjct:   183 WKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPL 242

Query:   269 MLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFL 328
             MLW+PH P+YP+L+K   +GL  EETKEMR RGL  P L KL +NG Y ++V  VR+ F 
Sbjct:   243 MLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFE 302

Query:   329 VSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
               E+VR+DC  +  SD K+IG KL+++VPC+ + F+ EQI++WRGK
Sbjct:   303 TEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILWRGK 348

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2061604 CAF1 [Arabidopsis thaliana (taxid:3702)]

 Score = 767 (275.1 bits), Expect = 3.9e-76, P = 3.9e-76
 Identities = 158/332 (47%), Positives = 213/332 (64%)

Query:    93 PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
             PF+F+YSYTET + V+P+ LREP Y+PFGP  + R WTG                    P
Sbjct:   150 PFEFKYSYTETPK-VKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLPP 208

Query:   136 AADPKVKSAEE-GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
                  +K  ++ G   P +  + +  +E I GEPLT  E + LV  C +  T RQ+N+GR
Sbjct:   209 VGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLK--TTRQLNMGR 266

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DGLTHNMLN+IH+ WK     +IKC GV TVDM NVC QLE+K  GK+I+R GG L L+R
Sbjct:   267 DGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFR 326

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNYN + RP  PLMLW+P  PVYP+LI+   EGL+ +E   MR++G  +  + KL KNG
Sbjct:   327 GRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNG 386

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
              Y  LV  V++AF V ELVRIDCQG++ SD++KIG KL+DLVPC+LV+FE EQI++WRG+
Sbjct:   387 VYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIWRGR 446

Query:   375 DYKHPGDDGQFFTHRELFDDPENDSACGVEEE 406
             ++K            ++ +D E D+A   ++E
Sbjct:   447 EWKSSLTTPD--KKGDILEDIEVDTALPEDDE 476

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0000373 "Group II intron splicing" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

TAIR|locus:2028100 CAF2 [Arabidopsis thaliana (taxid:3702)]

 Score = 732 (262.7 bits), Expect = 2.0e-72, P = 2.0e-72
 Identities = 152/303 (50%), Positives = 200/303 (66%)

Query:    93 PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA--------PAAD-----P 139
             PF+F++SY+ET + V+P+G+REP + PF P  + R WTG           P  D     P
Sbjct:   110 PFEFQFSYSETPK-VKPVGIREPAFMPFAPPTMPRPWTGKAPLKKSKKKIPLFDSFNPPP 168

Query:   140 KVKSAEEGAEDPN-LE----EKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
               KS  +  E P  L      K  + RE + GEPL   E+  L+ K H +   RQ+NLGR
Sbjct:   169 AGKSGVKYVEMPGPLPFGRYPKEGMNREEVLGEPLKRWEKGMLI-KPHMH-DNRQVNLGR 226

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DG THNML  IH+HWK     +++C GVPTVDM NVC  LE+KT G+II R GG + L+R
Sbjct:   227 DGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLFR 286

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNYN + RP  PLMLW+P  PVYPKLI+   EGL+ EE  E R +G ++  + KL+KNG
Sbjct:   287 GRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKNG 346

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQIVVWRGK 374
              Y SLV  VRDAF +S LV++DC GLE SDYKKIG KL++LVPC+L++F+ EQI++WRG+
Sbjct:   347 VYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQILMWRGR 406

Query:   375 DYK 377
             ++K
Sbjct:   407 EWK 409

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0000373 "Group II intron splicing" evidence=IDA

TAIR|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 2.5e-11, Sum P(2) = 2.5e-11
 Identities = 28/74 (37%), Positives = 45/74 (60%)

Query:   185 RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIF 244
             R  +++ +G+ G+T  ++N IH  W+  E V+I C  +  ++MK     LE KT G +I+
Sbjct:   180 RLTKKLKIGKAGITEGIVNGIHERWRTTEVVKIFCEDISRMNMKRTHDVLETKTGGLVIW 239

Query:   245 RHGGTLVLYRGRNY 258
             R G  ++LYRG NY
Sbjct:   240 RSGSKILLYRGVNY 253

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;RCA

GO:0000372 "Group I intron splicing" evidence=IMP

GO:0000373 "Group II intron splicing" evidence=IMP

TAIR|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 7.3e-10, Sum P(2) = 7.3e-10
 Identities = 45/147 (30%), Positives = 73/147 (49%)

Query:   139 PKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKR-------QIN 191
             P  K+ EE A +  + E  + V ++ +    + AE    VE     R +R       +IN
Sbjct:   206 PWEKNEEEQAAERVVGEGGVAVMQKRRARAPSLAE--LTVEDSELRRLRRDGMYLRVRIN 263

Query:   192 LGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLV 251
             + + GLT  ++  I++ W+  E VR+K   V   DMK     +E +T G +I+R G  +V
Sbjct:   264 IPKAGLTQAVMEKIYDTWRKEELVRLKFHEVLARDMKTAHEIVERRTGGMVIWRAGSVMV 323

Query:   252 LYRGRNYNPKKRPVIPLMLWRPHEPVY 278
             +YRG +Y  K  PVI   +  P E ++
Sbjct:   324 VYRGLDY--KGPPVISNQMAGPKETLF 348

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

TAIR|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 4.4e-09, Sum P(2) = 4.4e-09
 Identities = 32/90 (35%), Positives = 49/90 (54%)

Query:   169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
             L  +E + L     R  +K +I  G  G+T   ++ I   WK AE VR+K  G   ++M+
Sbjct:   221 LPESELRRLRNLTFRTASKMRIRGG--GVTQVAVDAIKEKWKSAEIVRLKIEGASALNMR 278

Query:   229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNY 258
              +   LE KT G +I+R G ++ LYRG +Y
Sbjct:   279 KMHEILEKKTGGLVIWRSGTSISLYRGVSY 308

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0000373 "Group II intron splicing" evidence=IMP

GO:0048316 "seed development" evidence=IGI

TAIR|locus:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]

 Score = 127 (49.8 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 30/122 (24%), Positives = 64/122 (52%)

Query:   185 RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIF 244
             + K  + +G  G+   ++ ++H HWK  E V++ C   P   +K +   +   + G +I 
Sbjct:   106 KNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMIARLSGGVVIN 165

Query:   245 RHG-GTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEG--LSIEETKE-MRKR 300
              H   T++++RGRNY   K  +IP+      + ++    +  +E   L+I++T++ +R+ 
Sbjct:   166 IHNVKTIIMFRGRNYRQPKN-LIPVNTLTKRKALFKARFEQALESQKLNIKKTEQQLRRM 224

Query:   301 GL 302
             G+
Sbjct:   225 GV 226

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2181372 CRS1 "ortholog of maize chloroplast splicing factor CRS1" [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00052, Sum P(2) = 0.00052
 Identities = 37/127 (29%), Positives = 67/127 (52%)

Query:   138 DPKVKSAEE-GAEDP-NLEEKRILVRERIQGEPL-TNAER---KALVEKCHRNRTKRQ-- 189
             + KV+S +  G + P   EE+R ++R R++ E + T AE    + L+ +  R  +K +  
Sbjct:   167 EEKVESKDRFGGKMPWEREEERFILR-RMKKESVPTTAELILDEGLLNRLRREASKMRKW 225

Query:   190 INLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTV-DMKNVCFQLEDKTFGKIIFRHGG 248
             +N+ + G+T  ++N I + WK  E   ++   VP   +M+     +E KT G ++     
Sbjct:   226 VNVRKAGVTELVVNKIKSMWKLNELAMVR-FDVPLCRNMERAQEIIEMKTGGLVVLSKKE 284

Query:   249 TLVLYRG 255
              LV+YRG
Sbjct:   285 FLVVYRG 291

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0000373 "Group II intron splicing" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6Z4U2	CAF1M_ORYSJ	No assigned EC number	0.6763	0.7943	0.7850	yes	no
Q8VYD9	CAF1M_ARATH	No assigned EC number	0.7054	0.9267	0.9679	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00026315001 SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (418 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	423
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	3e-26
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	4e-24
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	4e-15
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	5e-13
COG1534	97	COG1534, COG1534, Predicted RNA-binding protein co	8e-05

>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain

 Score =  100 bits (252), Expect = 3e-26
 Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +R+ L    H    K  + +G++GLT  ++ +I    +  E +++K LG    D K
Sbjct: 1   LTGKQRRYLRSLAHH--LKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR 254
            +  +L +KT  +++   G T+VLYR
Sbjct: 59  EIAEELAEKTGAELVQVIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly

 Score = 94.8 bits (237), Expect = 4e-24
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L    H    K  + +G++GLT  +L +I    +  E +++K LG    D K
Sbjct: 1   LTGKQKRYLRSLAHH--LKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR 254
            +  +L ++T  +++   G T+VLYR
Sbjct: 59  EIAEELAEETGAELVQVIGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly

 Score = 69.8 bits (172), Expect = 4e-15
 Identities = 19/84 (22%), Positives = 42/84 (50%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ KNG    ++  + +A    EL+++   G +R D K+I
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 349 GCKLRDLVPCILVTFEKEQIVVWR 372
             +L +     LV    + IV++R
Sbjct: 61  AEELAEETGAELVQVIGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain

 Score = 64.0 bits (157), Expect = 5e-13
 Identities = 20/84 (23%), Positives = 41/84 (48%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ KNG    +V  + +A    EL+++   G +R D K+I
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 349 GCKLRDLVPCILVTFEKEQIVVWR 372
             +L +     LV      IV++R
Sbjct: 61  AEELAEKTGAELVQVIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl|CDD|224451 COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L  K H  +   QI  G++GLT  ++ +I    +  E +++K L     D K
Sbjct: 2   LTGKQKRFLRSKAHHLKPIVQI--GKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR-GRNYNPKKRPV 265
            +   L ++T  +++   G TLVLYR  +       P 
Sbjct: 60  EIAEALAEETGAELVQVIGKTLVLYRESKEKRKISLPR 97

Length = 97

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	423
PRK10343	97	RNA-binding protein YhbY; Provisional	99.95
PRK10343	97	RNA-binding protein YhbY; Provisional	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.95
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.95
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.94
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.66
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.1

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=6.7e-28  Score=204.08  Aligned_cols=89  Identities=25%  Similarity=0.298  Sum_probs=86.9

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEE
Q 014482          167 EPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRH  246 (423)
Q Consensus       167 e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~I  246 (423)
                      |+||++|+++||++||  +|+|+|+|||+|||++|+++|+++|++|||||||+++++.++.++++++|+++|||++||+|
T Consensus         1 m~Lt~kqr~~LR~~ah--~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I   78 (97)
T PRK10343          1 MNLSTKQKQHLKGLAH--PLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI   78 (97)
T ss_pred             CCCCHHHHHHHHHhcC--CCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee
Confidence            5799999999999998  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEeccCC
Q 014482          247 GGTLVLYRGRN  257 (423)
Q Consensus       247 G~viVLYRg~n  257 (423)
                      |+++||||++.
T Consensus        79 G~~~vlYR~~~   89 (97)
T PRK10343         79 GKTLVLYRPTK   89 (97)
T ss_pred             CcEEEEEecCC
Confidence            99999999974

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=1.1e-27  Score=202.86  Aligned_cols=89  Identities=15%  Similarity=0.184  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      +||+||++|||++||+|+|+|+|||+|++++++++|++||++||||||+|++++.+|.+++|++|++.|||++||+||++
T Consensus         2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~   81 (97)
T PRK10343          2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKT   81 (97)
T ss_pred             CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcE
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCC
Q 014482          368 IVVWRGKDY  376 (423)
Q Consensus       368 IVLYRgk~~  376 (423)
                      +||||.++.
T Consensus        82 ~vlYR~~~~   90 (97)
T PRK10343         82 LVLYRPTKE   90 (97)
T ss_pred             EEEEecCCC
Confidence            999999863

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=1.6e-27  Score=200.93  Aligned_cols=90  Identities=18%  Similarity=0.254  Sum_probs=87.6

Q ss_pred             CCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCEE
Q 014482          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQI  368 (423)
Q Consensus       289 LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~I  368 (423)
                      ||+||++|||++||+|+|+++|||+|++++++++|++||++||||||++++++.+|.+++|++|++.|||++||+||+++
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~   80 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI   80 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCCCC
Q 014482          369 VVWRGKDYKH  378 (423)
Q Consensus       369 VLYRgk~~~p  378 (423)
                      ||||++++.+
T Consensus        81 vlYR~~~~~~   90 (95)
T TIGR00253        81 VLYRPTKERK   90 (95)
T ss_pred             EEEecCCccC
Confidence            9999987543

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain

Probab=99.95  E-value=1.9e-27  Score=194.92  Aligned_cols=84  Identities=36%  Similarity=0.543  Sum_probs=75.4

Q ss_pred             CCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEcc
Q 014482          169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG  248 (423)
Q Consensus       169 LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~  248 (423)
                      ||++|+++||++||  +++|+|+|||+|||++|+++|+++|++||||||||.+++.++++++|++|+++|||++||++|+
T Consensus         1 Lt~ke~~~Lr~~a~--~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~   78 (84)
T PF01985_consen    1 LTSKERKFLRKLAH--HLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGR   78 (84)
T ss_dssp             --HHHHHHHHHHHT--TC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETT
T ss_pred             CCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECC
Confidence            79999999999998  9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEec
Q 014482          249 TLVLYR  254 (423)
Q Consensus       249 viVLYR  254 (423)
                      ++||||
T Consensus        79 ~~vlyR   84 (84)
T PF01985_consen   79 TIVLYR   84 (84)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            999998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=3.6e-27  Score=198.89  Aligned_cols=87  Identities=26%  Similarity=0.379  Sum_probs=85.2

Q ss_pred             CCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEcc
Q 014482          169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG  248 (423)
Q Consensus       169 LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG~  248 (423)
                      ||++|+++||++||  +|+|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|+++|||++||+||+
T Consensus         1 Lt~kqr~~Lr~~ah--~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~   78 (95)
T TIGR00253         1 LTGKQKRHLRGKAH--HLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGK   78 (95)
T ss_pred             CCHHHHHHHHHHhC--CCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEcc
Confidence            79999999999998  9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeccCC
Q 014482          249 TLVLYRGRN  257 (423)
Q Consensus       249 viVLYRg~n  257 (423)
                      ++||||++.
T Consensus        79 ~~vlYR~~~   87 (95)
T TIGR00253        79 TIVLYRPTK   87 (95)
T ss_pred             EEEEEecCC
Confidence            999999963

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain

Probab=99.94  E-value=1.1e-26  Score=190.50  Aligned_cols=84  Identities=27%  Similarity=0.372  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCEE
Q 014482          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQI  368 (423)
Q Consensus       289 LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~I  368 (423)
                      ||++|+++||++|++|+|+++|||+|+|++++++|+++|++||||||+|++++..|.+++|++|++.|||++||++|+++
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~   80 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI   80 (84)
T ss_dssp             --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEc
Q 014482          369 VVWR  372 (423)
Q Consensus       369 VLYR  372 (423)
                      ||||
T Consensus        81 vlyR   84 (84)
T PF01985_consen   81 VLYR   84 (84)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=7.9e-26  Score=191.41  Aligned_cols=87  Identities=29%  Similarity=0.463  Sum_probs=84.8

Q ss_pred             CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (423)
Q Consensus       168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG  247 (423)
                      +||++|+++||+.||  +++|+|+|||+|||++|+.+|+++|++||||||++++++.+|.+++|+.|++.+||++||+||
T Consensus         1 ~Lt~kq~~~Lrs~Ah--~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG   78 (97)
T COG1534           1 MLTGKQKRFLRSKAH--HLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIG   78 (97)
T ss_pred             CCcHHHHHHHHHhhc--cCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeee
Confidence            589999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeccC
Q 014482          248 GTLVLYRGR  256 (423)
Q Consensus       248 ~viVLYRg~  256 (423)
                      +++||||.+
T Consensus        79 ~~~vlyr~~   87 (97)
T COG1534          79 KTLVLYRES   87 (97)
T ss_pred             eEEEEEecC
Confidence            999999943

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=6e-26  Score=192.16  Aligned_cols=91  Identities=20%  Similarity=0.289  Sum_probs=87.8

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      +||+||+++||++||++.|+|+|||||++++++++|+++|++||||||++++++..|.+++|++|++.+||++||+||++
T Consensus         1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~   80 (97)
T COG1534           1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT   80 (97)
T ss_pred             CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCC
Q 014482          368 IVVWRGKDYKH  378 (423)
Q Consensus       368 IVLYRgk~~~p  378 (423)
                      +||||.+.++.
T Consensus        81 ~vlyr~~~e~~   91 (97)
T COG1534          81 LVLYRESKEKR   91 (97)
T ss_pred             EEEEecCcccc
Confidence            99999665553

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=99.66  E-value=1.3e-16  Score=169.32  Aligned_cols=220  Identities=19%  Similarity=0.142  Sum_probs=194.3

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCC-eEEE
Q 014482          166 GEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG-KIIF  244 (423)
Q Consensus       166 ~e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTgg-eVVq  244 (423)
                      .+.+...+..+||..|-  .+.-.+  +++|+|+++++.|++.|+.+|+++++|....+..|....+.++..|++ -+||
T Consensus        11 ~~~~~~~~~~~l~~~~~--~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~   86 (564)
T KOG1990|consen   11 ELTVDEADLRRLRLVAT--GMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVW   86 (564)
T ss_pred             HhhcCHHHHHHHhhhhc--cceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeee
Confidence            45688999999999995  666555  999999999999999999999999999999999999999999999999 9999


Q ss_pred             EEccEEEEeccCCCCCC----CCC---c--------------------ccccccCC--CCCCCcCcccccC---------
Q 014482          245 RHGGTLVLYRGRNYNPK----KRP---V--------------------IPLMLWRP--HEPVYPKLIKTTI---------  286 (423)
Q Consensus       245 ~IG~viVLYRg~nY~p~----~Rp---k--------------------IpLm~Wk~--~~Pv~p~ll~~~~---------  286 (423)
                      +.|-....|++..|.-+    .|-   .                    -.+++|+.  ..|++.++++.++         
T Consensus        87 ~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~  166 (564)
T KOG1990|consen   87 SRGDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRT  166 (564)
T ss_pred             ecCccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhcc
Confidence            99999988866665421    111   1                    12369994  4899999987754         


Q ss_pred             ------CCCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEe-cCCCcccHHHHHHHH--HhhcC
Q 014482          287 ------EGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDC-QGLERSDYKKIGCKL--RDLVP  357 (423)
Q Consensus       287 ------e~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~v-l~n~~~D~keia~eL--aelTg  357 (423)
                            ..||.++..++|.+|..++|+|.+|.++..++++..+...|++++++|+.| ++.+......+|.++  ...+|
T Consensus       167 l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg  246 (564)
T KOG1990|consen  167 LPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTG  246 (564)
T ss_pred             CCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcC
Confidence                  499999999999999999999999999999999999999999999999998 788999999999999  99999


Q ss_pred             CEEEEEeCCEEEEEcCCCCCCCCCCcccchhccc
Q 014482          358 CILVTFEKEQIVVWRGKDYKHPGDDGQFFTHREL  391 (423)
Q Consensus       358 ~~lVq~iG~~IVLYRgk~~~p~~v~~~~~~ere~  391 (423)
                      ..||..++..+|+||+++|.+ .+ .+.+.+++.
T Consensus       247 ~~lv~hN~~~dv~y~~~~Fl~-~l-p~~l~~f~~  278 (564)
T KOG1990|consen  247 KVLVLHNKLLDVMYRYKNFLS-PL-PSTLEEFTD  278 (564)
T ss_pred             CeEEeeccceeeeeehhhccc-cc-chhHHHhhh
Confidence            999999999999999999999 77 777777776

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]

Probab=99.10  E-value=1.1e-10  Score=124.55  Aligned_cols=213  Identities=21%  Similarity=0.272  Sum_probs=174.4

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChH-hHHHHHHHH--HHhhCCeEE
Q 014482          167 EPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTV-DMKNVCFQL--EDKTFGKII  243 (423)
Q Consensus       167 e~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~-dmkeiae~L--eekTggeVV  243 (423)
                      ..|+..+.-.+|.++.  .+.+.+.+|.++.-.++...+...|+.|+.+|+.|...-.. ....++..+  -..+|+.||
T Consensus       173 ~~l~~~~~~~~r~~~~--~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv  250 (564)
T KOG1990|consen  173 PLLTSIESTLLRRLGY--KLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLV  250 (564)
T ss_pred             hhhhhHHHHHHHHhcc--cccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEE
Confidence            5699999999999997  89999999999999999999999999999999888854443 444677777  889999999


Q ss_pred             EEEccEEEEeccCCCCCC--------CC-----Ccccc--------------------------cccCCC----------
Q 014482          244 FRHGGTLVLYRGRNYNPK--------KR-----PVIPL--------------------------MLWRPH----------  274 (423)
Q Consensus       244 q~IG~viVLYRg~nY~p~--------~R-----pkIpL--------------------------m~Wk~~----------  274 (423)
                      .+.+-..|+||+++|-.+        ++     |.+..                          -.|...          
T Consensus       251 ~hN~~~dv~y~~~~Fl~~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~  330 (564)
T KOG1990|consen  251 LHNKLLDVMYRYKNFLSPLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRL  330 (564)
T ss_pred             eeccceeeeeehhhcccccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchh
Confidence            999999999998887541        11     11100                          012110          


Q ss_pred             --------------------------------------CCCCcCcccccCCCCCHHHHHHHHHcCCCCCceEEeccCCch
Q 014482          275 --------------------------------------EPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYY  316 (423)
Q Consensus       275 --------------------------------------~Pv~p~ll~~~~e~LT~KQr~yLR~lA~~l~PifqLGKnGv~  316 (423)
                                                            .+--+-.....++.+|.+++.+++++|..+....-+|+.|+.
T Consensus       331 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f  410 (564)
T KOG1990|consen  331 KLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVF  410 (564)
T ss_pred             hhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccc
Confidence                                                  000011122456799999999999999999999999999999


Q ss_pred             hhHHHHHHHHHhcCceEEEEecCCCc-ccHHHHHHHHHhhcCCEEEEEeCC-E---EEEEcCCCCCCCCC
Q 014482          317 GSLVPMVRDAFLVSELVRIDCQGLER-SDYKKIGCKLRDLVPCILVTFEKE-Q---IVVWRGKDYKHPGD  381 (423)
Q Consensus       317 ~~Lv~~V~eAlEkrELVKI~vl~n~~-~D~keia~eLaelTg~~lVq~iG~-~---IVLYRgk~~~p~~v  381 (423)
                      .+++.+.+.+|..+|++|+.|+.-.. ...++.|..+....|..+|+++.. .   |+.||+++|.-+..
T Consensus       411 ~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~  480 (564)
T KOG1990|consen  411 DGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTS  480 (564)
T ss_pred             cceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcc
Confidence            99999999999999999999966554 999999999999999999998744 3   79999999988755

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	423
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	1e-19
1rq8_A	104	Conserved hypothetical protein; structural genomic	2e-18
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           L+  +++ L  K   +     + LG +GLT  +L +I N   H E +++K  G      +
Sbjct: 3   LSTKQKQFL--KGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
            +   +  +T    +   G  LVLYR    + + +  +P
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRP---SEEAKIQLP 96

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104

 Score = 78.9 bits (195), Expect = 2e-18
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L  +   +       +G+ G+  NM+  I +  ++ E +++  L     D K
Sbjct: 2   LTGKQKRYL--RSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHE 275
            +   L + T  +++   G  +V+YR      K+   I L L   H 
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRES----KENKEIELPLEHHHH 102

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 48.7 bits (115), Expect = 3e-06
 Identities = 77/460 (16%), Positives = 131/460 (28%), Gaps = 137/460 (29%)

Query: 36  SSKLYDHYSFKPPP---------SLSPKPENP-----NPTLNPNKNF-KKKSKPQYRPPS 80
           S +  DH                +L  K E          L  N  F     K + R PS
Sbjct: 47  SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS 106

Query: 81  SLDAPKKKYTDLPFDFRYSYTETNQNVRPIGL-REPKYSPFGPGRLEREWTGVCAPAADP 139
                 + Y +     R      NQ      + R   Y      +L R+      PA   
Sbjct: 107 ---MMTRMYIE----QRDRLYNDNQVFAKYNVSRLQPYL-----KL-RQALLELRPA--K 151

Query: 140 KV---------KS--AEEGAEDPNLEEKR------ILVRERIQG----EPLTNAERKALV 178
            V         K+  A +      ++ K       + ++         E L     +   
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 179 EKC----HRNRTKRQINLGRDGLTHNM-----------LNDIHNHWKHAEAVRIKC--LG 221
                  H +  K +I+  +  L   +           L ++  + K   A  + C  L 
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-QNAKAWNAFNLSCKIL- 269

Query: 222 VPTVDMKNVCFQLEDKTFGKII-------FRHGGTL-VLYRGRNYNPKKRP-----VIPL 268
           + T   K V   L   T   I                +L +  +  P+  P       P 
Sbjct: 270 LTTRF-KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328

Query: 269 ML----------------WRPHEPVYPKL---IKTTIEGLSIEETKEMRKRGLAV----- 304
            L                W+       KL   I++++  L   E ++M  R L+V     
Sbjct: 329 RLSIIAESIRDGLATWDNWK--HVNCDKLTTIIESSLNVLEPAEYRKMFDR-LSVFPPSA 385

Query: 305 --P--VLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCIL 360
             P  +L+ +  +        MV    +V++L +     L     K+    +  +   + 
Sbjct: 386 HIPTILLSLIWFDVIKS--DVMV----VVNKLHK---YSLVEKQPKESTISIPSIYLELK 436

Query: 361 VTFEKE-----QIV----VWRGKDYKH---PGDDGQFFTH 388
           V  E E      IV    + +  D      P  D  F++H
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	423
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.96
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.96
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.96
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.95

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=99.96  E-value=2.2e-29  Score=211.85  Aligned_cols=87  Identities=25%  Similarity=0.374  Sum_probs=85.7

Q ss_pred             CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (423)
Q Consensus       168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG  247 (423)
                      +||++|+++||++||  +|+|+|+|||+|||++|+++|++||++||||||+|++++.+|++++|++|+++|||++||+||
T Consensus         2 ~Lt~kqr~~Lr~~ah--~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG   79 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAH--HLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIG   79 (98)
T ss_dssp             CCCHHHHHHHHHHHT--TBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeccC
Q 014482          248 GTLVLYRGR  256 (423)
Q Consensus       248 ~viVLYRg~  256 (423)
                      +++||||++
T Consensus        80 ~~~vLyR~~   88 (98)
T 1jo0_A           80 HILVLYRPS   88 (98)
T ss_dssp             TEEEEECCC
T ss_pred             CEEEEEccC
Confidence            999999987

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1

Probab=99.96  E-value=2.9e-29  Score=213.41  Aligned_cols=88  Identities=22%  Similarity=0.395  Sum_probs=86.3

Q ss_pred             CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (423)
Q Consensus       168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG  247 (423)
                      |||++|+++||++||  +|+|+|+|||+|||++|+++|+++|++||||||||++++.+|++++|++|+++|||++||+||
T Consensus         1 mLt~kqr~~LR~~ah--~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG   78 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAH--NIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (104)
T ss_dssp             CCCHHHHHHHHHHTT--SSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeccCC
Q 014482          248 GTLVLYRGRN  257 (423)
Q Consensus       248 ~viVLYRg~n  257 (423)
                      +++||||++.
T Consensus        79 ~~~VLYR~~~   88 (104)
T 1rq8_A           79 SMIVIYRESK   88 (104)
T ss_dssp             TEEEEEECCC
T ss_pred             CEEEEEeCCC
Confidence            9999999875

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1

Probab=99.96  E-value=3.1e-29  Score=213.27  Aligned_cols=93  Identities=16%  Similarity=0.224  Sum_probs=90.0

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      |||+||++|||++|++|+|+|+|||+|++++++++|++||++||||||+|+++|..|.+++|++|++.|||++||+||++
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~   80 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM   80 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCCCC
Q 014482          368 IVVWRGKDYKHPG  380 (423)
Q Consensus       368 IVLYRgk~~~p~~  380 (423)
                      +||||+++.++..
T Consensus        81 ~VLYR~~~~~~~i   93 (104)
T 1rq8_A           81 IVIYRESKENKEI   93 (104)
T ss_dssp             EEEEECCCSCCSC
T ss_pred             EEEEeCCCCCCce
Confidence            9999999866543

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=99.95  E-value=9.5e-29  Score=207.99  Aligned_cols=89  Identities=16%  Similarity=0.203  Sum_probs=87.4

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      .||+||++|||++||+|+|+|+|||+|++++++++|++||++||||||+|+++|..|.+++|++|++.|||++||+||++
T Consensus         2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG~~   81 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI   81 (98)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCC
Q 014482          368 IVVWRGKDY  376 (423)
Q Consensus       368 IVLYRgk~~  376 (423)
                      +||||+++.
T Consensus        82 ~vLyR~~~~   90 (98)
T 1jo0_A           82 LVLYRPSEE   90 (98)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEccCCC
Confidence            999999965

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	423
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	4e-24
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	6e-13
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-22
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	1e-11

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 93.6 bits (233), Expect = 4e-24
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L    H         +G+ G+  NM+  I +  ++ E +++  L     D K
Sbjct: 2   LTGKQKRYLRSLAHN--IDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPK 261
            +   L + T  +++   G  +V+YR    N +
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRESKENKE 92

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 62.0 bits (151), Expect = 6e-13
 Identities = 15/89 (16%), Positives = 36/89 (40%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ K G   +++  + D     EL+++        D K++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 349 GCKLRDLVPCILVTFEKEQIVVWRGKDYK 377
              L +     LV      IV++R     
Sbjct: 62  AETLSEATRSELVQVIGSMIVIYRESKEN 90

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

 Score = 88.6 bits (220), Expect = 3e-22
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           L+  +++ L  K   +     + LG +GLT  +L +I N   H E +++K  G      +
Sbjct: 3   LSTKQKQFL--KGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
            +   +  +T    +   G  LVLYR    + + +  +P
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRP---SEEAKIQLP 96

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 14/87 (16%), Positives = 35/87 (40%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           LS ++ + ++     +  +  L  NG    ++  + +A    EL+++   G +R   + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 349 GCKLRDLVPCILVTFEKEQIVVWRGKD 375
              +        V      +V++R  +
Sbjct: 63  INAIVRETKAAQVQTIGHILVLYRPSE 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	423
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.96
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.95
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.95
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.95

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

Probab=99.96  E-value=8.3e-29  Score=204.95  Aligned_cols=90  Identities=22%  Similarity=0.390  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (423)
Q Consensus       168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG  247 (423)
                      +||++|+++||++||  +|+|+|+|||+|||++|+++|+++|++||||||+|.+++..|+++++++|+++|||++||+||
T Consensus         1 mLt~kqr~~LR~~ah--~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG   78 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAH--NIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (96)
T ss_dssp             CCCHHHHHHHHHHTT--SSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CcCHHHHHHHHHHhc--CCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeccCCCC
Q 014482          248 GTLVLYRGRNYN  259 (423)
Q Consensus       248 ~viVLYRg~nY~  259 (423)
                      +++||||+++++
T Consensus        79 ~~~vlyR~~~~~   90 (96)
T d1rq8a_          79 SMIVIYRESKEN   90 (96)
T ss_dssp             TEEEEEECCCSC
T ss_pred             CEEEEEeCCCCC
Confidence            999999997543

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=99.95  E-value=3.2e-28  Score=201.73  Aligned_cols=88  Identities=25%  Similarity=0.373  Sum_probs=86.0

Q ss_pred             CCCHHHHHHHHHHhhhCCCCccEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhhCCeEEEEEc
Q 014482          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (423)
Q Consensus       168 ~LT~kErk~LRk~Ah~~~LkPvV~IGK~GLT~~VV~eI~~aLk~hELVKIK~l~~~~~dmkeiae~LeekTggeVVq~IG  247 (423)
                      +||++|+++||++||  +|+|+|+|||+|||++|+++|+++|+.||||||+|.+++.+|+++++++|+++|||.|||+||
T Consensus         2 tLt~kqr~~LR~~ah--~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG   79 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAH--HLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIG   79 (97)
T ss_dssp             CCCHHHHHHHHHHHT--TBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEeccCC
Q 014482          248 GTLVLYRGRN  257 (423)
Q Consensus       248 ~viVLYRg~n  257 (423)
                      +++||||++.
T Consensus        80 ~~~ilYR~~~   89 (97)
T d1jo0a_          80 HILVLYRPSE   89 (97)
T ss_dssp             TEEEEECCCS
T ss_pred             CEEEEEcCCC
Confidence            9999999864

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

Probab=99.95  E-value=1.2e-28  Score=203.97  Aligned_cols=93  Identities=16%  Similarity=0.224  Sum_probs=90.4

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      |||+||++|||++||+|+|+++|||+|+|++++++|++||++||||||+|++++..|.+++|++|++.|||++||+||++
T Consensus         1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~   80 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM   80 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred             CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCCCC
Q 014482          368 IVVWRGKDYKHPG  380 (423)
Q Consensus       368 IVLYRgk~~~p~~  380 (423)
                      +||||++++++..
T Consensus        81 ~vlyR~~~~~~ki   93 (96)
T d1rq8a_          81 IVIYRESKENKEI   93 (96)
T ss_dssp             EEEEECCCSCCSC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999999877653

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=99.95  E-value=5.1e-28  Score=200.52  Aligned_cols=89  Identities=16%  Similarity=0.203  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHcCCCCCceEEeccCCchhhHHHHHHHHHhcCceEEEEecCCCcccHHHHHHHHHhhcCCEEEEEeCCE
Q 014482          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRDLVPCILVTFEKEQ  367 (423)
Q Consensus       288 ~LT~KQr~yLR~lA~~l~PifqLGKnGv~~~Lv~~V~eAlEkrELVKI~vl~n~~~D~keia~eLaelTg~~lVq~iG~~  367 (423)
                      .||+||++|||++||+|+|+|+|||+|+|++++++|++||++||||||+|++++..|.+++|++|++.|||++||+||++
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG~~   81 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI   81 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCC
Q 014482          368 IVVWRGKDY  376 (423)
Q Consensus       368 IVLYRgk~~  376 (423)
                      +||||+++.
T Consensus        82 ~ilYR~~~~   90 (97)
T d1jo0a_          82 LVLYRPSEE   90 (97)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999999863